3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>PDB Viewing</title>
27 <strong>Viewing PDB Structures</strong>
29 Jalview can be used to view protein structures by following the steps below:
31 <li>Select the <strong>"View Structure"</strong> option from a
32 sequence's <a href="../menus/popupMenu.html">pop-up menu</a> to invoke the <a href="structurechooser.html">Structure Chooser</a> interface.
34 <li>If one or more structures exists for the given sequence, the <a href="structurechooser.html">Structure Chooser</a>
35 dialogue is opened with a list of the found structures meta-data.</li>
36 <li>However, if no structure was found, the <a href="structurechooser.html">Structure Chooser</a> interface is opened with options for manual association of PDB structures.</li>
39 <li>Choose the structure to view from the discovered list. This can be done either manually by clicking directly
40 on the desired structure(s) in the list, or automatically by
41 using the drop-down menu on the interface to filter and auto-select the best structure based on certain
42 criteria like quality, resolution, etc.</li>
43 <li>When the desired structure(s) have been selected, they can be
44 viewed by clicking the <strong>"View"</strong> button below the summary list.
50 <a href="jmol.html">Jmol viewer</a> has been included since Jalview
51 2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>, provided it is
52 installed and can be launched by Jalview. The default viewer can be
54 <a href="preferences.html#structure">Structure tab</a> in the
55 <strong>Tools→Preferences</strong> dialog box.
57 Structure data imported into Jalview can also be processed to display
58 secondary structure and temperature factor annotation. See the <a
59 href="xsspannotation.html">Annotation from Structure</a> page for
63 <p>The following menu entries are provided for viewing structure data
65 <li>The <strong>"Structure→View
66 Structure→</strong> submenu allows a single PDB structure to be chosen
67 for display from the available structures for a sequence.
69 <li>The <strong>"Structure→View all <em>N</em>
71 </strong> option will open a new window containing all structures associated
72 with the current selection, superposed according to the currently selected region of the alignment.<br/><em>This
73 capability was added in Jalview 2.7</em>
75 <li>The <strong>"Structure→View all <em>N</em>
76 representative structures
77 </strong> option will open a new window containing exactly one structure per
78 currently selected sequence.<br />
79 <em>The View representative structures option was introduced in
80 Jalview 2.8.1</em></li>
84 <p>If a <strong>single</strong> pdb
85 structure is selected, one of the following will happen:</p>
88 <li>If no structures are open, then an interactive display of the
89 structure will be opened in a new window.</li>
91 <li>If another structure is already shown for the current
92 alignment, then you will be asked if you want to add and <a
93 href="jmol.html#align">align this structure</a> to the structure in
94 the existing view. (<em>new feature in Jalview 2.6</em>).</li>
96 <li>If the structure is already shown, then you will be prompted
97 to associate the sequence with an existing view of the selected
98 structure. This is useful when working with multi-domain or multi-chain PDB files.</li>
100 <li style="list-style: none">See the <a href="jmol.html">Jmol
101 </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
105 <p><strong>Importing PDB Entries or files in PDB format</strong><br>
106 You can retrieve sequences from the PDB using the <a
107 href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with
108 this service are automatically associated with their source database
109 entry. For PDB sequences, simply select PDB as the database and enter
110 your known PDB id (appended with ':' and a chain code, if desired).<br>
111 Jalview will also read PDB files directly. Simply load in the file as
112 you would an alignment file. The sequences of any peptide chains will be
113 extracted from the file and viewed in the alignment window.</p>
116 <strong>Associating a large number of PDB files to sequences
117 in an alignment</strong><br /> It is often the case when working with
118 structure alignments that you will have a directory of PDB files, and
119 an alignment involving one or more of the structures. If you drag a
120 number of PDB files onto an alignment in the Jalview desktop, Jalview
121 will give you the option of associating PDB files with sequences that
122 have the same filename. This means, for example, you can automatically
123 associate PDB files with names like '1gaq.pdb' with sequences that
124 have an ID like '1gaq'.
125 <br/><em>Note: This feature was added in Jalview 2.7</em>
127 <p><em>Note for jalview applet users:<br>
128 Due to the applet security constraints, PDB Files can currently only be
129 imported by cut and paste of the PDB file text into the text box opened
130 by the 'From File' entry of the structure menu.</em></p>
132 <p><strong>Viewing the PDB Residue Numbering</strong><br>
133 Sequences which have PDB entry or PDB file associations are annotated
134 with sequence features from a group named with the associated PDB
135 accession number or file name. Each feature gives the corresponding PDB
136 Residue Number for each mapped residue in the sequence. The display of
137 these features is controlled through the <strong>"View→Sequence
138 Features"</strong> menu item and the <a href="featuresettings.html">Feature
139 Settings dialog box</a>.</p>
141 <p><em><strong>Outstanding problem with cut'n'pasted
142 files in Jalview 2.6 and Jalview 2.7</strong><br>
143 Structures imported via the cut'n'paste dialog box will not be correctly
144 highlighted or coloured when they are displayed in structure views,
145 especially if they contain more than one PDB structure. See the bug
146 report at http://issues.jalview.org/browse/JAL-623 for news on this problem.</em></p>